Question: When I am trying to copy 9GB BAM files to the hard disk, the copied BAM file has only 4GB.What could be the issue?
0
gravatar for bioinforesearchquestions
2.8 years ago by
United States
bioinforesearchquestions270 wrote:

Hello friends,

I have multiple BAM files in my server, each of them is 9GB file. When I am trying to copy them to the hard disk, the copied BAM file has only 4GB. I tried multiple times, what could be the issue?

When I opened the BAM file, I could see alignment only till chr8.

bam alignment dnaseq • 1.0k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by bioinforesearchquestions270
2

What filesystem is the hard drive you're using? Some of the older ones (I think FAT32) can only store 4GB files as a maximum. I'd check this first. If you're using NTFS (or OSX Journaled) you should be fine, and it'll be some other issue.

ADD REPLYlink written 2.8 years ago by Joe16k

Thanks, Jrj.healey.

To test this, I tried copying the BAM file to my local machine from the remote server. I could see the 9GB BAM file in my local machine :)

ADD REPLYlink written 2.8 years ago by bioinforesearchquestions270
2

If you need a DOS filesystem compatible drive partition for some reason, the exFAT file system will enable both OSX and MS-DOS to read and write. I format most of my USB sticks with this so that I can connect it to any machine.

ADD REPLYlink written 2.8 years ago by Joe16k

Thanks, Jrj.healey. Just now, I did it.

ADD REPLYlink written 2.8 years ago by bioinforesearchquestions270
1

Either a 32bit file system or you ran out of space.

ADD REPLYlink written 2.8 years ago by Devon Ryan94k

Thanks, Devon for your suggestions

ADD REPLYlink written 2.8 years ago by bioinforesearchquestions270
3
gravatar for WouterDeCoster
2.8 years ago by
Belgium
WouterDeCoster43k wrote:

Are you working on a fat32 partition with a maximum of 4Gb? Reformatting to e.g. exFAT would fix this.

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by WouterDeCoster43k

Thanks WouterDecoster.

I have a Mac OS machine. I used both 128GB usb drive and 500GB hard disk, by default it has been formatted on MS-DOS (FAT32).

Now I get it. I forgot to reformat the new drive and disk.

ADD REPLYlink written 2.8 years ago by bioinforesearchquestions270

Alright, glad my first guess was right. For good measure I have moved my comment to an answer and added formatting, as such we can mark this question as solved.

ADD REPLYlink written 2.8 years ago by WouterDeCoster43k
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